SNP set test results on Crohn’s disease (CD) using different SNP weights.

<p>(A) Manhattan plot shows association signal across genes (x-axis) detected by SNP set tests using three different sets of SNP weights. EqualWeight (black): equal SNP weights. HC (red): SNP weights constructed using the estimated coefficient parameters for continuous histone mark based annotations in the GWAS consortium study. HB (green): SNP weights constructed using the estimated coefficient parameters for binary histone mark based annotations in the GWAS consortium study. The gold dashed line represents genome-wide significance threshold (8.95x10^-6). (B) The same results are displayed with QQ plot of -log10 p-values. Grey shaded area represents the 95% point-wise confidence interval.